In one of the most serious breaches in coalition unity, Nick Clegg today repudiated David Cameron's refusal to refer his culture secretary Jeremy Hunt to the adviser on the ministerial code, and ordered his MPs not to defend Cameron's decision in the Commons on Wednesday.

It is only the second time that Liberal Democrat MPs have been ordered not to vote with the Tories in the Commons since the coalition was formed in May 2010.

Lib Dem sources said the deputy prime minister had been at loggerheads with the prime minister over his handling of Hunt for weeks and had repeatedly told Cameron that the culture secretary may have to be referred to Sir Alex Allan, the adviser on the ministerial code.

The sources said Clegg was angry that Cameron decided to clear Hunt within minutes of the culture secretary giving evidence to the Leveson inquiry a fortnight ago. Clegg believed Hunt's answers showed that questions over his handling of News Corp's bid for BSkyB had not been cleared up.

The sources said the unanswered questions included whether Hunt had given accurate answers to MPs over the extent of his lobbying for News Corp, and whether Hunt had adhered to the ministerial code by allowing his special adviser, Adam Smith, to have extensive contacts with News Corp lobbyists.

The Leveson inquiry has said that it is not in a position to judge whether the ministerial code has been breached.

Lib Dem sources said their MPs would abstain on a Labour motion in the Commons on Wednesday calling for Hunt to be referred to Allan. Clegg, who is giving evidence to the Leveson inquiry on Wednesday, wants to show that his party did not develop cosy relations with News Corp.

The Lib Dems said they would not be backing the Labour motion because it was for Cameron alone to decide whether to refer someone to Allan. They did not want to be seen to side with a Labour party that had used special advisers such as Damian McBride, who worked with former Labour prime minister Gordon Brown.

The only previous time the Liberal Democrats have broken ranks with their coalition colleagues was over a motion condemning Cameron's use of the veto at the EU summit in December.

Clegg told Cameron of his decision before meeting his MPs in Westminster. No Lib Dem MP dissented from Clegg's decision, which is as much a repudiation of Cameron's own judgment on a critical issue of good governance as it is of Hunt's behaviour.

A senior Tory aide played down tensions with the Lib Dems, saying their decision over the debate was "not unexpected".

"It's a party political motion not government business," the aide said.

The shadow culture secretary, Harriet Harman, said: "This is an important opportunity for the House of Commons to make clear the importance it places on secretaries of state being transparent and truthful to parliament.

"I think members from all sides of the house will want to be sure that this issue is not simply swept under the carpet. Misleading parliament is not just some outdated constitutional issue – it matters."

Labour is unlikely to win the vote, despite the Lib Dems' abstention. Even if the motion is passed, it would only be a symbolic blow to Cameron, as he retains the final say over whether his independent adviser investigates a minister.

When asked, A Lib Dem source said: "We are not jumping on Jeremy Hunt's corpse, but there are still questions left unanswered. Nick has made his views known directly face to face and repeatedly to Cameron."

Some Tories are also known to be uneasy at the way in which Cameron has refused to refer Hunt to Allan, whereas Lady Warsi, the co-chair of the Conservative party, has been referred to the adviser on a relatively trivial charge after she apologised for failing to properly declare business dealings with her husband's cousin.